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Yorodumi- PDB-5l8r: The structure of plant photosystem I super-complex at 2.6 angstro... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5l8r | ||||||||||||
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| Title | The structure of plant photosystem I super-complex at 2.6 angstrom resolution. | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / photosynthesis / membrane complex / chlorophyll / light harvesting | ||||||||||||
| Function / homology | Function and homology informationphotosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / photosynthesis, light harvesting / chloroplast thylakoid lumen / chloroplast envelope ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / photosynthesis, light harvesting / chloroplast thylakoid lumen / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein stabilization / protein domain specific binding / magnesium ion binding / metal ion binding / nucleus Similarity search - Function | ||||||||||||
| Biological species | Pisum sativum (garden pea) | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||||||||
Authors | Mazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N. | ||||||||||||
| Funding support | Israel, 3items
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Citation | Journal: Nat Plants / Year: 2017Title: Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution. Authors: Mazor, Y. / Borovikova, A. / Caspy, I. / Nelson, N. | ||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5l8r.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5l8r.ent.gz | 1.6 MB | Display | PDB format |
| PDBx/mmJSON format | 5l8r.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5l8r_validation.pdf.gz | 54 MB | Display | wwPDB validaton report |
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| Full document | 5l8r_full_validation.pdf.gz | 54.7 MB | Display | |
| Data in XML | 5l8r_validation.xml.gz | 261.8 KB | Display | |
| Data in CIF | 5l8r_validation.cif.gz | 293.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8r ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8r | HTTPS FTP |
-Related structure data
| Related structure data | |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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| Unit cell |
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Components
-Protein , 5 types, 5 molecules 12CDG
| #1: Protein | Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS |
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| #2: Protein | Mass: 28912.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038 |
| #7: Protein | Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I |
| #8: Protein | Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS |
| #11: Protein | Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9S7N7*PLUS |
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34
| #3: Protein | Mass: 29634.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904 |
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| #4: Protein | Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2 |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
| #5: Protein | Mass: 84265.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310, photosystem I |
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| #6: Protein | Mass: 82512.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0F6NGI2, photosystem I |
-Putative uncharacterized ... , 2 types, 2 molecules EL
| #9: Protein | Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6 |
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| #16: Protein | Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1 |
-Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK
| #10: Protein | Mass: 17238.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12 |
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| #12: Protein | Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL10 |
| #13: Protein/peptide | Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227 |
| #14: Protein/peptide | Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3 |
| #15: Protein | Mass: 7988.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3 |
-Sugars , 2 types, 15 molecules 


| #24: Sugar | ChemComp-LMT / #26: Sugar | ChemComp-DGD / |
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-Non-polymers , 13 types, 436 molecules 
























| #17: Chemical | ChemComp-LUT / ( #18: Chemical | ChemComp-BCR / #19: Chemical | ChemComp-CLA / #20: Chemical | ChemComp-CHL / #21: Chemical | ChemComp-LHG / #22: Chemical | ChemComp-LMG / #23: Chemical | #25: Chemical | #27: Chemical | ChemComp-CL0 / | #28: Chemical | #29: Chemical | #30: Chemical | ChemComp-ZEX / ( | #31: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.75 Details: 30mM Tris-Hcl pH8.75, 50mM KH2PO4, 0.03% Octyl Glucose Neopentyl Glycol, 14% PEG400, 2mM glutathione |
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
| Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2015 |
| Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.6→50 Å / Num. obs: 248807 / % possible obs: 99.9 % / Redundancy: 84.6 % / CC1/2: 0.997 / Net I/σ(I): 9.8 |
| Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 83.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.4 |
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Processing
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| Refinement | Method to determine structure: SAD / Resolution: 2.6→39.906 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27 / Stereochemistry target values: MLHL
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.6→39.906 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Origin x: 15.038 Å / Origin y: 7.6729 Å / Origin z: 64.5628 Å
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| Refinement TLS group | Selection details: all |
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Pisum sativum (garden pea)
X-RAY DIFFRACTION
Israel, 3items
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